1,174 research outputs found
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
To explain the observed dynamics in equilibrium single-molecule measurements
of biomolecules, the experimental observable is often chosen as a putative
reaction coordinate along which kinetic behavior is presumed to be governed by
diffusive dynamics. Here, we invoke the splitting probability as a test of the
suitability of such a proposed reaction coordinate. Comparison of the observed
splitting probability with that computed from the kinetic model provides a
simple test to reject poor reaction coordinates. We demonstrate this test for a
force spectroscopy measurement of a DNA hairpin
Food legumes in cropping systems and farmers participatory approaches
Food legumes or pulses are an important component of cropping systems and provide an
opportunity to increase food supplies, particularly in the developing world, in a sustainable
way, through intensifying and diversifying agricultural systems. Food legumes are more
positive crops, in terms of resource conservation, than cereals and a rotation of food legumes
with cereals makes cereal production more economic and sustainable. In the developing
world legumes is a major source of nutrition for the poor. However, in the past three decades
the production of food legumes has-gradually fallen in comparison
,
with a rapid growth in
cereals, and livestock products. Yields of the majority of the legumes have stagnated as they
have been relegated to more marginal and unfavorable environments; and no major yield
breakthroughs have been apparent . Concurrently, the first generation of Green Revolution
Technologies used to increase food production are being reduced in effectiveness and have
become unable economically to sustain the present, or desired increased levels in productivity.
This is due, in part, to the increasing dominance of monocropping with cereals and the
subsequent displacement of legumes. The role of food legumes as a key component of
second-generation green revolution technologies is therefore crucial and timely. Large
variations in yields are presently experienced which is compounded by intense biotic and
abiotic stresses, and an inadequate supporting policy environment. We review the potential
role of legumes in cropping systems in developing countries and make little effort to
distinguish between cool and warm-season pulses as trends in supply and demand have been similar and most factors influence both types of pulses. Recent examples of
diversification of cereal based cropping system emphasizing farmer participatory approaches
are discussed
Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model
The conformation and the phase diagram of a membrane protein are investigated
via grand canonical ensemble approach using a homopolymer model. We discuss the
nature and pathway of -helix integration into the membrane that results
depending upon membrane permeability and polymer adsorptivity. For a membrane
with the permeability larger than a critical value, the integration becomes the
second order transition that occurs at the same temperature as that of the
adsorption transition. For a nonadsorbing membrane, the integration is of the
first order due to the aggregation of -helices.Comment: RevTeX with 5 postscript figure
Correlates of Complete Childhood Vaccination in East African Countries.
Despite the benefits of childhood vaccinations, vaccination rates in low-income countries (LICs) vary widely. Increasing coverage of vaccines to 90% in the poorest countries over the next 10 years has been estimated to prevent 426 million cases of illness and avert nearly 6.4 million childhood deaths worldwide. Consequently, we sought to provide a comprehensive examination of contemporary vaccination patterns in East Africa and to identify common and country-specific barriers to complete childhood vaccination. Using data from the Demographic and Health Surveys (DHS) for Burundi, Ethiopia, Kenya, Rwanda, Tanzania, and Uganda, we looked at the prevalence of complete vaccination for polio, measles, Bacillus Calmette-Guérin (BCG) and DTwPHibHep (DTP) as recommended by the WHO among children ages 12 to 23 months. We conducted multivariable logistic regression within each country to estimate associations between complete vaccination status and health care access and sociodemographic variables using backwards stepwise regression. Vaccination varied significantly by country. In all countries, the majority of children received at least one dose of a WHO recommended vaccine; however, in Ethiopia, Tanzania, and Uganda less than 50% of children received a complete schedule of recommended vaccines. Being delivered in a public or private institution compared with being delivered at home was associated with increased odds of complete vaccination status. Sociodemographic covariates were not consistently associated with complete vaccination status across countries. Although no consistent set of predictors accounted for complete vaccination status, we observed differences based on region and the location of delivery. These differences point to the need to examine the historical, political, and economic context of each country in order to maximize vaccination coverage. Vaccination against these childhood diseases is a critical step towards reaching the Millennium Development Goal of reducing under-five mortality by two-thirds by 2015 and thus should be a global priority
Hamiltonian walks on Sierpinski and n-simplex fractals
We study Hamiltonian walks (HWs) on Sierpinski and --simplex fractals. Via
numerical analysis of exact recursion relations for the number of HWs we
calculate the connectivity constant and find the asymptotic behaviour
of the number of HWs. Depending on whether or not the polymer collapse
transition is possible on a studied lattice, different scaling relations for
the number of HWs are obtained. These relations are in general different from
the well-known form characteristic of homogeneous lattices which has thus far
been assumed to hold for fractal lattices too.Comment: 22 pages, 6 figures; final versio
Error threshold in optimal coding, numerical criteria and classes of universalities for complexity
The free energy of the Random Energy Model at the transition point between
ferromagnetic and spin glass phases is calculated. At this point, equivalent to
the decoding error threshold in optimal codes, free energy has finite size
corrections proportional to the square root of the number of degrees. The
response of the magnetization to the ferromagnetic couplings is maximal at the
values of magnetization equal to half. We give several criteria of complexity
and define different universality classes. According to our classification, at
the lowest class of complexity are random graph, Markov Models and Hidden
Markov Models. At the next level is Sherrington-Kirkpatrick spin glass,
connected with neuron-network models. On a higher level are critical theories,
spin glass phase of Random Energy Model, percolation, self organized
criticality (SOC). The top level class involves HOT design, error threshold in
optimal coding, language, and, maybe, financial market. Alive systems are also
related with the last class. A concept of anti-resonance is suggested for the
complex systems.Comment: 17 page
Statics, metastable states and barriers in protein folding: A replica variational approach
Protein folding is analyzed using a replica variational formalism to
investigate some free energy landscape characteristics relevant for dynamics. A
random contact interaction model that satisfies the minimum frustration
principle is used to describe the coil-globule transition (characterized by
T_CG), glass transitions (by T_A and T_K) and folding transition (by T_F).
Trapping on the free energy landscape is characterized by two characteristic
temperatures, one dynamic, T_A the other static, T_K (T_A> T_K), which are
similar to those found in mean field theories of the Potts glass. 1)Above T_A,
the free energy landscape is monotonous and polymer is melted both dynamically
and statically. 2)Between T_A and T_K, the melted phase is still dominant
thermodynamically, but frozen metastable states, exponentially large in number,
appear. 3)A few lowest minima become thermodynamically dominant below T_K,
where the polymer is totally frozen. In the temperature range between T_A and
T_K, barriers between metastable states are shown to grow with decreasing
temperature suggesting super-Arrhenius behavior in a sufficiently large system.
Due to evolutionary constraints on fast folding, the folding temperature T_F is
expected to be higher than T_K, but may or may not be higher than T_A. Diverse
scenarios of the folding kinetics are discussed based on phase diagrams that
take into account the dynamical transition, as well as the static ones.Comment: 41 pages, LaTeX, 9 EPS figure
Modeling study on the validity of a possibly simplified representation of proteins
The folding characteristics of sequences reduced with a possibly simplified
representation of five types of residues are shown to be similar to their
original ones with the natural set of residues (20 types or 20 letters). The
reduced sequences have a good foldability and fold to the same native structure
of their optimized original ones. A large ground state gap for the native
structure shows the thermodynamic stability of the reduced sequences. The
general validity of such a five-letter reduction is further studied via the
correlation between the reduced sequences and the original ones. As a
comparison, a reduction with two letters is found not to reproduce the native
structure of the original sequences due to its homopolymeric features.Comment: 6 pages with 4 figure
Atomic-scale modeling of the deformation of nanocrystalline metals
Nanocrystalline metals, i.e. metals with grain sizes from 5 to 50 nm, display
technologically interesting properties, such as dramatically increased
hardness, increasing with decreasing grain size. Due to the small grain size,
direct atomic-scale simulations of plastic deformation of these materials are
possible, as such a polycrystalline system can be modeled with the
computational resources available today.
We present molecular dynamics simulations of nanocrystalline copper with
grain sizes up to 13 nm. Two different deformation mechanisms are active, one
is deformation through the motion of dislocations, the other is sliding in the
grain boundaries. At the grain sizes studied here the latter dominates, leading
to a softening as the grain size is reduced. This implies that there is an
``optimal'' grain size, where the hardness is maximal.
Since the grain boundaries participate actively in the deformation, it is
interesting to study the effects of introducing impurity atoms in the grain
boundaries. We study how silver atoms in the grain boundaries influence the
mechanical properties of nanocrystalline copper.Comment: 10 pages, LaTeX2e, PS figures and sty files included. To appear in
Mater. Res. Soc. Symp. Proc. vol 538 (invited paper). For related papers, see
http://www.fysik.dtu.dk/~schiotz/publist.htm
Nucleation phenomena in protein folding: The modulating role of protein sequence
For the vast majority of naturally occurring, small, single domain proteins
folding is often described as a two-state process that lacks detectable
intermediates. This observation has often been rationalized on the basis of a
nucleation mechanism for protein folding whose basic premise is the idea that
after completion of a specific set of contacts forming the so-called folding
nucleus the native state is achieved promptly. Here we propose a methodology to
identify folding nuclei in small lattice polymers and apply it to the study of
protein molecules with chain length N=48. To investigate the extent to which
protein topology is a robust determinant of the nucleation mechanism we compare
the nucleation scenario of a native-centric model with that of a sequence
specific model sharing the same native fold. To evaluate the impact of the
sequence's finner details in the nucleation mechanism we consider the folding
of two non- homologous sequences. We conclude that in a sequence-specific model
the folding nucleus is, to some extent, formed by the most stable contacts in
the protein and that the less stable linkages in the folding nucleus are solely
determined by the fold's topology. We have also found that independently of
protein sequence the folding nucleus performs the same `topological' function.
This unifying feature of the nucleation mechanism results from the residues
forming the folding nucleus being distributed along the protein chain in a
similar and well-defined manner that is determined by the fold's topological
features.Comment: 10 Figures. J. Physics: Condensed Matter (to appear
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