1,163 research outputs found
Designability of lattice model heteropolymers
Protein folds are highly designable, in the sense that many sequences fold to
the same conformation. In the present work we derive an expression for the
designability in a 20 letter lattice model of proteins which, relying only on
the Central Limit Theorem, has a generality which goes beyond the simple model
used in its derivation. This expression displays an exponential dependence on
the energy of the optimal sequence folding on the given conformation measured
with respect to the lowest energy of the conformational dissimilar structures,
energy difference which constitutes the only parameter controlling
designability. Accordingly, the designability of a native conformation is
intimately connected to the stability of the sequences folding to them.Comment: in press on Phys. Rev.
The generalized non-conservative model of a 1-planet system - revisited
We study the long-term dynamics of a planetary system composed of a star and
a planet. Both bodies are considered as extended, non-spherical, rotating
objects. There are no assumptions made on the relative angles between the
orbital angular momentum and the spin vectors of the bodies. Thus, we analyze
full, spatial model of the planetary system. Both objects are assumed to be
deformed due to their own rotations, as well as due to the mutual tidal
interactions. The general relativity corrections are considered in terms of the
post-Newtonian approximation. Besides the conservative contributions to the
perturbing forces, there are also taken into account non-conservative effects,
i.e., the dissipation of the mechanical energy. This dissipation is a result of
the tidal perturbation on the velocity field in the internal zones with
non-zero turbulent viscosity (convective zones). Our main goal is to derive the
equations of the orbital motion as well as the equations governing
time-evolution of the spin vectors (angular velocities). We derive the
Lagrangian equations of the second kind for systems which do not conserve the
mechanical energy. Next, the equations of motion are averaged out over all fast
angles with respect to time-scales characteristic for conservative
perturbations. The final equations of motion are then used to study the
dynamics of the non-conservative model over time scales of the order of the age
of the star. We analyze the final state of the system as a function of the
initial conditions. Equilibria states of the averaged system are finally
discussed.Comment: 37 pages, 13 figures, accepted to Celestial Mechanics and Dynamical
Astronom
Half-metallic antiferromagnets in thiospinels
We have theoretically designed the half-metallic (HM) antiferromagnets (AFMs)
in thiospinel systems, and , based on the electronic structure
studies in the local-spin-density approximation (LSDA). We have also explored
electronic and magnetic properties of parent spinel compounds of the above
systems; and are found to be HM
ferromagnets in their cubic spinel structures, while is a
ferrimagnetic insulator. We have discussed the feasibility of material
synthesis of HM-AFM thiospinel systems.Comment: 4 pages, 5 figure
On the spherical-axial transition in supernova remnants
A new law of motion for supernova remnant (SNR) which introduces the quantity
of swept matter in the thin layer approximation is introduced. This new law of
motion is tested on 10 years observations of SN1993J. The introduction of an
exponential gradient in the surrounding medium allows to model an aspherical
expansion. A weakly asymmetric SNR, SN1006, and a strongly asymmetric SNR,
SN1987a, are modeled. In the case of SN1987a the three observed rings are
simulated.Comment: 19 figures and 14 pages Accepted for publication in Astrophysics &
Space Science in the year 201
Landscape equivalent of the shoving model
It is shown that the shoving model expression for the average relaxation time
of viscous liquids follows largely from a classical "landscape" estimation of
barrier heights from curvature at energy minima. The activation energy involves
both instantaneous bulk and shear moduli, but the bulk modulus contributes less
than 8% to the temperature dependence of the activation energy. This reflects
the fact that the physics of the two models are closely related.Comment: 4 page
Common and gender-specific associations with cocaine use on gray matter volume: Data from the ENIGMA addiction working group
Common and gender-specific associations with cocaine use on gray matter volume: Data from the ENIGMA addiction working group
Gray matter volume (GMV) in frontal cortical and limbic regions is susceptible to cocaine-associated reductions in cocaine-dependent individuals (CD) and is negatively associated with duration of cocaine use. Gender differences in CD individuals have been reported clinically and in the context of neural responses to cue-induced craving and stress reactivity. The variability of GMV in select brain areas between men and women (e.g., limbic regions) underscores the importance of exploring interaction effects between gender and cocaine dependence on brain structure. Therefore, voxel-based morphometry data derived from the ENIGMA Addiction Consortium were used to investigate potential gender differences in GMV in CD individuals compared to matched controls (CTL). T1-weighted MRI scans and clinical data were pooled from seven sites yielding 420 gender- and age-matched participants: CD men (CDM, n = 140); CD women (CDW, n = 70); control men (CTLM, n = 140); and control women (CTLW, n = 70). Differences in GMV were assessed using a 2 × 2 ANCOVA, and voxelwise whole-brain linear regressions were conducted to explore relationships between GMV and duration of cocaine use. All analyses were corrected for age, total intracranial volume, and site. Diagnostic differences were predominantly found in frontal regions (CD < CTL). Interestingly, gender × diagnosis interactions in the left anterior insula and left lingual gyrus were also documented, driven by differences in women (CDW < CTLW). Further, lower right hippocampal GMV was associated with greater cocaine duration in CDM. Given the importance of the anterior insula to interoception and the hippocampus to learning contextual associations, results may point to gender-specific mechanisms in cocaine addiction
Embedding a Native State into a Random Heteropolymer Model: The Dynamic Approach
We study a random heteropolymer model with Langevin dynamics, in the
supersymmetric formulation. Employing a procedure similar to one that has been
used in static calculations, we construct an ensemble in which the affinity of
the system for a native state is controlled by a "selection temperature" T0. In
the limit of high T0, the model reduces to a random heteropolymer, while for
T0-->0 the system is forced into the native state. Within the Gaussian
variational approach that we employed previously for the random heteropolymer,
we explore the phases of the system for large and small T0. For large T0, the
system exhibits a (dynamical) spin glass phase, like that found for the random
heteropolymer, below a temperature Tg. For small T0, we find an ordered phase,
characterized by a nonzero overlap with the native state, below a temperature
Tn \propto 1/T0 > Tg. However, the random-globule phase remains locally stable
below Tn, down to the dynamical glass transition at Tg. Thus, in this model,
folding is rapid for temperatures between Tg and Tn, but below Tg the system
can get trapped in conformations uncorrelated with the native state. At a lower
temperature, the ordered phase can also undergo a dynamical glass transition,
splitting into substates separated by large barriers.Comment: 19 pages, revtex, 6 figure
The long-time dynamics of two hydrodynamically-coupled swimming cells
Swimming micro-organisms such as bacteria or spermatozoa are typically found
in dense suspensions, and exhibit collective modes of locomotion qualitatively
different from that displayed by isolated cells. In the dilute limit where
fluid-mediated interactions can be treated rigorously, the long-time
hydrodynamics of a collection of cells result from interactions with many other
cells, and as such typically eludes an analytical approach. Here we consider
the only case where such problem can be treated rigorously analytically, namely
when the cells have spatially confined trajectories, such as the spermatozoa of
some marine invertebrates. We consider two spherical cells swimming, when
isolated, with arbitrary circular trajectories, and derive the long-time
kinematics of their relative locomotion. We show that in the dilute limit where
the cells are much further away than their size, and the size of their circular
motion, a separation of time scale occurs between a fast (intrinsic) swimming
time, and a slow time where hydrodynamic interactions lead to change in the
relative position and orientation of the swimmers. We perform a multiple-scale
analysis and derive the effective dynamical system - of dimension two -
describing the long-time behavior of the pair of cells. We show that the system
displays one type of equilibrium, and two types of rotational equilibrium, all
of which are found to be unstable. A detailed mathematical analysis of the
dynamical systems further allows us to show that only two cell-cell behaviors
are possible in the limit of , either the cells are attracted to
each other (possibly monotonically), or they are repelled (possibly
monotonically as well), which we confirm with numerical computations
Quantum mechanics: Myths and facts
A common understanding of quantum mechanics (QM) among students and practical
users is often plagued by a number of "myths", that is, widely accepted claims
on which there is not really a general consensus among experts in foundations
of QM. These myths include wave-particle duality, time-energy uncertainty
relation, fundamental randomness, the absence of measurement-independent
reality, locality of QM, nonlocality of QM, the existence of well-defined
relativistic QM, the claims that quantum field theory (QFT) solves the problems
of relativistic QM or that QFT is a theory of particles, as well as myths on
black-hole entropy. The fact is that the existence of various theoretical and
interpretational ambiguities underlying these myths does not yet allow us to
accept them as proven facts. I review the main arguments and counterarguments
lying behind these myths and conclude that QM is still a
not-yet-completely-understood theory open to further fundamental research.Comment: 51 pages, pedagogic review, revised, new references, to appear in
Found. Phy
- …