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, $\rm Mn(CrV)S_{4}$ and $\rm Fe_{0.5}Cu_{0.5}(V_{0.5}Ti_{1.5})S_{4}$, 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; $\rm CuV_{2}S_{4}$ and $\rm CuTi_{2}S_{4}$ are found to be HM ferromagnets in their cubic spinel structures, while $\rm MnCr_{2}S_{4}$ 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

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 $t\to\infty$, 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