Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of the aggregation prone ($N^*$) states, which are rarely populated under force free native conditions, but are encoded in the spectrum of native fluctuations. The folding phase diagrams of SH3 as a function of denaturant concentration ($[C]$), mechanical force ($f$), and temperature exhibit an apparent two-state behavior, without revealing the presence of the elusive $N^*$ states. Interestingly, the phase boundaries separating the folded and unfolded states at all [C] and $f$ fall on a master curve, which can can be quantitatively described using an analogy to superconductors in a magnetic field. The free energy profiles as a function of the molecular extension ($R$), which are accessible in pulling experiments, ($R$), reveal the presence of a native-like $N^*$ with a disordered solvent-exposed amino terminal $\beta$-strand. The structure of the $N^*$ state is identical to that found in Fyn SH3 by NMR dispersion experiments. We show that the time scale for fibril formation can be estimated from the population of the $N^*$ state, determined by the free energy gap separating the native structure and the $N^*$ state, a finding that can be used to assess fibril forming tendencies of proteins. The structures of the $N^*$ state are used to show that oligomer formation and likely route to fibrils occur by a domain-swap mechanism in SH3 domain.Comment: 12 pages, 8 figures, 9 supplementary figures (on 5 more pages), 2 supplementary movies (on youtube

Chromomagnetic instability in two-flavor quark matter at nonzero temperature

We calculate the effective potential of the 2SC/g2SC phases including vector condensates ($$and$$) and study the gluonic phase and the single plane-wave Larkin-Ovchinnikov-Fulde-Ferrell state at nonzero temperature. Our analysis is performed within the framework of the gauged Nambu--Jona-Lasinio model. We compute potential curvatures with respect to the vector condensates and investigate the temperature dependence of the Meissner masses squared of gluons of color 4--7 and 8 in the neutral 2SC/g2SC phases. The phase diagram is presented in the plane of temperature and coupling strength. The unstable regions for gluons 4--7 and 8 are mapped out on the phase diagram. We find that, apart from the case of strong coupling, the 2SC/g2SC phases at low temperatures are unstable against the vector condensation until the temperature reaches tens of MeV.Comment: 10 pages, 10 figures, revisions to text, published in Phys. Rev.

Relativistic BCS-BEC crossover in a boson-fermion model

We investigate the crossover from Bardeen-Cooper-Schrieffer (BCS) pairing to a Bose-Einstein condensate (BEC) in a relativistic superfluid within a boson-fermion model. The model includes, besides the fermions, separate bosonic degrees of freedom, accounting for the bosonic nature of the Cooper pairs. The crossover is realized by tuning the difference between the boson mass and boson chemical potential as a free parameter. The model yields populations of condensed and uncondensed bosons as well as gapped and ungapped fermions throughout the crossover region for arbitrary temperatures. Moreover, we observe the appearance of antiparticles for sufficiently large values of the crossover parameter. As an application, we study pairing of fermions with imbalanced populations. The model can potentially be applied to color superconductivity in dense quark matter at strong couplings.Comment: ReVTex4, 19 pages, 10 figures; new chapter added about the case of imbalanced fermion populations; minor modifications to main part; references adde

Superficial temporal artery aneurysms

AbstractObjective: We analyzed the data from our vascular registry to determine the cause, clinical features, and cost-effective management of this uncommon pathologic entity. Design: Patients referred to the vascular surgery outpatient clinic of a tertiary referral center during the past 18 years were evaluated. Subjects: The subjects were six male patients (14 to 32 years) referred for evaluation of a unilateral pulsatile mass over the temporal region of the head. Intervention: Diagnosis of superficial temporal artery aneurysm was verified by loss of the aneurysm's pulse with compression of the ipsilateral proximal superficial temporal artery. All treated aneurysms were electively ligated and excised as an ambulatory procedure. Results: The symptoms were resolved. No recurrences or other complications were seen. Conclusions: Although rare, a superficial temporal artery aneurysm should be considered when a temporal head mass is evaluated. This condition is almost always a result of blunt or penetrating head trauma. Clinical examination is sufficient to confirm the diagnosis. Simple elective ligation and excision of the aneurysm is curative. (J Vasc Surg 1998;27:374-7.

Color-flavor locked superconductor in a magnetic field

We study the effects of moderately strong magnetic fields on the properties of color-flavor locked color superconducting quark matter in the framework of the Nambu-Jona-Lasinio model. We find that the energy gaps, which describe the color superconducting pairing as well as the magnetization, are oscillating functions of the magnetic field. Also, we observe that the oscillations of the magnetization can be so strong that homogeneous quark matter becomes metastable for a range of parameters. We suggest that this points to the possibility of magnetic domains or other types of magnetic inhomogeneities in the quark cores of magnetars.Comment: 12 pages, 3 figures. Version accepted for publication in Phys. Rev.

Collective excitations, instabilities, and ground state in dense quark matter

We study the spectrum of light plasmons in the (gapped and gapless) two-flavor color superconducting phases and its connection with the chromomagnetic instabilities and the structure of the ground state. It is revealed that the chromomagnetic instabilities in the 4-7th and 8th gluonic channels correspond to two very different plasmon spectra. These spectra lead us to the unequivocal conclusion about the existence of gluonic condensates (some of which can be spatially inhomogeneous) in the ground state. We also argue that spatially inhomogeneous gluonic condensates should exist in the three-flavor quark matter with the values of the mass of strange quark corresponding to the gapless color-flavor locked state.Comment: Revtex, 5 pages, 4 figures, two figures and clarifications added, to appear in PRD (Rapid Communications

A low energy theory for superfluid and solid matter and its application to the neutron star crust

We formulate a low energy effective theory describing phases of matter that are both solid and superfluid. These systems simultaneously break translational symmetry and the phase symmetry associated with particle number. The symmetries restrict the combinations of terms that can appear in the effective action and the lowest order terms featuring equal number of derivatives and Goldstone fields are completely specified by the thermodynamic free energy, or equivalently by the long-wavelength limit of static correlation functions in the ground state. We show that the underlying interaction between particles that constitute the lattice and the superfluid gives rise to entrainment, and mixing between the Goldstone modes. As a concrete example we discuss the low energy theory for the inner crust of a neutron star, where a lattice of ionized nuclei coexists with a neutron superfluid.Comment: 21 pages, 1 figur

Neutral Larkin--Ovchinnikov--Fulde--Ferrell state and chromomagnetic instability in two-flavor dense QCD

In two-flavor dense quark matter, we describe the dynamics in the single plane wave Larkin--Ovchinnikov--Fulde--Ferrell (LOFF) state satisfying the color and electric neutrality conditions. We find that because the neutral LOFF state itself suffers from a chromomagnetic instability in the whole region where it coexists with the (gapped/gapless) two-flavor superconducting (2SC/g2SC) phases, it cannot cure this instability in those phases. This is unlike the recently revealed gluonic phase which seems to be able to resolve this problem.Comment: Revtex4, 5 pages, 3 figures, clarifications added, to appear in Phys.Rev.Let

Gluonic phases, vector condensates, and exotic hadrons in dense QCD

We study the dynamics in phases with vector condensates of gluons (gluonic phases) in dense two-flavor quark matter. These phases yield an example of dynamics in which the Higgs mechanism is provided by condensates of gauge (or gauge plus scalar) fields. Because vacuum expectation values of spatial components of vector fields break the rotational symmetry, it is naturally to have a spontaneous breakdown both of external and internal symmetries in this case. In particular, by using the Ginzburg-Landau approach, we establish the existence of a gluonic phase with both the rotational symmetry and the electromagnetic U(1) being spontaneously broken. In other words, this phase describes an anisotropic medium in which the color and electric superconductivities coexist. It is shown that this phase corresponds to a minimum of the Ginzburg-Landau potential and, unlike the two-flavor superconducting (2SC) phase, it does not suffer from the chromomagnetic instability. The dual (confinement) description of its dynamics is developed and it is shown that there are light exotic vector hadrons in the spectrum, some of which condense. Because most of the initial symmetries in this system are spontaneously broken, its dynamics is very rich.Comment: 33 pages, RevTeX; v.2: Published PRD versio