284 research outputs found
Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
The equilibrium free energy landscape of off-lattice model heteropolymers as
a function of an internal coordinate, namely the end-to-end distance, is
reconstructed from out-of-equilibrium steered molecular dynamics data. This
task is accomplished via two independent methods: by employing an extended
version of the Jarzynski equality (EJE) and the inherent structure (IS)
formalism. A comparison of the free energies estimated with these two schemes
with equilibrium results obtained via the umbrella sampling technique reveals a
good quantitative agreement among all the approaches in a range of temperatures
around the ``folding transition'' for the two examined sequences. In
particular, for the sequence with good foldability properties, the mechanically
induced structural transitions can be related to thermodynamical aspects of
folding. Moreover, for the same sequence the knowledge of the landscape profile
allows for a good estimation of the life times of the native configuration for
temperatures ranging from the folding to the collapse temperature. For the
random sequence, mechanical and thermal unfolding appear to follow different
paths along the landscape.Comment: Latex manuscript, 20 pages, 23 figures, submitted to Physical Review
Reconstructing the free energy landscape of a mechanically unfolded model protein
The equilibrium free energy landscape of an off-lattice model protein as a
function of an internal (reaction) coordinate is reconstructed from
out-of-equilibrium mechanical unfolding manipulations. This task is
accomplished via two independent methods: by employing an extended version of
the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a
range of temperatures around the ``folding transition'' we find a good
quantitative agreement between the free energies obtained via EJE and IS
approaches. This indicates that the two methodologies are consistent and able
to reproduce equilibrium properties of the examined system. Moreover, for the
studied model the structural transitions induced by pulling can be related to
thermodynamical aspects of folding
Surface tension in bilayer membranes with fixed projected area
We study the elastic response of bilayer membranes with fixed projected area
to both stretching and shape deformations. A surface tension is associated to
each of these deformations. By using model amphiphilic membranes and computer
simulations, we are able to observe both the types of deformation, and thus,
both the surface tensions, related to each type of deformation, are measured
for the same system. These surface tensions are found to assume different
values in the same bilayer membrane: in particular they vanish for different
values of the projected area. We introduce a simple theory which relates the
two quantities and successfully apply it to the data obtained with computer
simulations
Probability density functions of work and heat near the stochastic resonance of a colloidal particle
We study experimentally and theoretically the probability density functions
of the injected and dissipated energy in a system of a colloidal particle
trapped in a double well potential periodically modulated by an external
perturbation. The work done by the external force and the dissipated energy are
measured close to the stochastic resonance where the injected power is maximum.
We show a good agreement between the probability density functions exactly
computed from a Langevin dynamics and the measured ones. The probability
density function of the work done on the particle satisfies the fluctuation
theorem
Minimal Detectable and Identifiable Biases for quality control
The Minimal Detectable Bias (MDB) is an important diagnostic tool in data quality control. The MDB is traditionally computed for the case of testing the null hypothesis against a single alternative hypothesis. In the actual practice of statistical testing and data quality control, however, multiple alternative hypotheses are considered. We show that this has two important consequences for one's interpretation and use of the popular MDB. First, we demonstrate that care should be exercised in using the single-hypothesis-based MDB for the multiple hypotheses case. Second, we show that for identification purposes, not the MDB, but the Minimal Identifiable Bias (MIB) should be used as the proper diagnostic tool. We analyse the circumstances that drive the differences between the MDBs and MIBs, show how they can be computed using Monte Carlo simulation and illustrate by means of examples the significant differences that one can experience between detectability and identifiability
Energetics and performance of a microscopic heat engine based on exact calculations of work and heat distributions
We investigate a microscopic motor based on an externally controlled
two-level system. One cycle of the motor operation consists of two strokes.
Within each stroke, the two-level system is in contact with a given thermal
bath and its energy levels are driven with a constant rate. The time evolution
of the occupation probabilities of the two states are controlled by one rate
equation and represent the system's response with respect to the external
driving. We give the exact solution of the rate equation for the limit cycle
and discuss the emerging thermodynamics: the work done on the environment, the
heat exchanged with the baths, the entropy production, the motor's efficiency,
and the power output. Furthermore we introduce an augmented stochastic process
which reflects, at a given time, both the occupation probabilities for the two
states and the time spent in the individual states during the previous
evolution. The exact calculation of the evolution operator for the augmented
process allows us to discuss in detail the probability density for the
performed work during the limit cycle. In the strongly irreversible regime, the
density exhibits important qualitative differences with respect to the more
common Gaussian shape in the regime of weak irreversibility.Comment: 21 pages, 7 figure
Discrete Breathers in a Realistic Coarse-Grained Model of Proteins
We report the results of molecular dynamics simulations of an off-lattice
protein model featuring a physical force-field and amino-acid sequence. We show
that localized modes of nonlinear origin (discrete breathers) emerge naturally
as continuations of a subset of high-frequency normal modes residing at
specific sites dictated by the native fold. In the case of the small
-barrel structure that we consider, localization occurs on the turns
connecting the strands. At high energies, discrete breathers stabilize the
structure by concentrating energy on few sites, while their collapse marks the
onset of large-amplitude fluctuations of the protein. Furthermore, we show how
breathers develop as energy-accumulating centres following perturbations even
at distant locations, thus mediating efficient and irreversible energy
transfers. Remarkably, due to the presence of angular potentials, the breather
induces a local static distortion of the native fold. Altogether, the
combination of this two nonlinear effects may provide a ready means for
remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog
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