The $\ensuremath{\gamma}$ decay from the ${2}_{3}^{+}$ state at about 2-MeV excitation in nuclei $^{140}\mathrm{Ba}$, $^{142}\mathrm{Ce}$, and $^{144}\mathrm{Nd}$, with 84 neutrons, is shown to be consistent its identification as lowest of mixed symmetry U(5) limit neutron-proton version interacting-boson model.

Abstract We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding aggregation. The systems are modeled using an all‐atom description of the chains with only torsional degrees freedom, implicit water. has modular structure that makes interaction potential easy to modify. currently implemented is able fold several peptides about 20 residues, also been used study aggregation force‐induced unfolding. simulation methods PROFASI Monte Carlo‐based...

Small oligomers formed early in the process of amyloid fibril formation may be major toxic species Alzheimer's disease. We investigate stages aggregation for tau fragment AcPHF6 (Ac-VQIVYK-NH2) using an implicit solvent all-atom model and extensive Monte Carlo simulations 12, 24, 36 chains. A variety small metastable aggregates form dissolve until aggregate a critical size conformation arises. However, stable oligomers, which are beta-sheet-rich feature many hydrophobic contacts, not always...

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The is two dimensional and has different ‘‘amino acids.’’ Using numerical simulations all chains containing eight or ten monomers, we examine sequence dependence at fixed temperature. It shown that only few exist in unique folded state this temperature, energy level spectra with types are compared. Furthermore, use as testbed improved Monte Carlo algorithms. Both algorithms based on letting some parameter...

The question of whether proteins originate from random sequences amino acids is addressed. A statistical analysis performed in terms blocked and walk values formed by binary hydrophobic assignments the along protein chains. Theoretical expectations these variables distributions hydrophobicities are compared with those obtained functional proteins. results, which based upon SWISS-PROT data base, convincingly show that acid differ what expected a statistically significant way. By performing...

The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. has only two types residues, hydrophobic and hydrophilic. In absence local interactions, native structure formation does not occur the temperatures considered. By including sequence independent which qualitatively reproduce properties functional proteins, dominance state many sequences observed. As in lattice approaches, takes place by gradual compactification, followed dependent transition....

We present results for static hadronic correlation functions in the high-temperature phase of QCD with four flavors dynamical quarks. confirm chiral-symmetry restoration through degeneracies spectrum screening lengths. also find that lengths \ensuremath{\rho} and N channels at T\ensuremath{\gtrsim}1.2${\mathit{T}}_{\mathit{c}}$ are close to a free quark gas.

We study the thermodynamic behavior of a model protein with 54 amino acids that forms three-helix bundle in its native state. The contains three types and five to six atoms per acid has Ramachandran torsional angles φ i , ψ as degrees freedom. force field is based on hydrogen bonds effective hydrophobicity forces. For suitable choice relative strength these interactions, we find three-helix-bundle undergoes an abrupt folding transition from expanded state Also shown corresponding one-...

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from (conformation-dependent) Gaussian distribution that favors approximately local deformations the chain. degree bias controlled by parameter b. tested on reduced model protein with 54 amino acids Ramachandran angles as its only degrees freedom, different Without excessive fine tuning, we find effective step size can be...

The unfolding behavior of ubiquitin under the influence a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed traces had simple two-state character, whereas others showed clear evidence intermediate states. Here, we use Monte Carlo simulations to investigate force-induced at atomic level. In agreement with experimental data, find that process can occur either in single step or through addition this randomness, many quantities,...

We describe and test an implicit solvent all-atom potential for simulations of protein folding aggregation. The is developed through studies structural thermodynamic properties 17 peptides with diverse secondary structure. Results obtained using the final form are presented all these peptides. same model, unchanged parameters, furthermore applied to a heterodimeric coiled-coil system, mixed alpha/beta three-helix-bundle protein, very good results. computational efficiency makes it possible...

Abstract The properties of the amyloid‐β peptide that lead to aggregation associated with Alzheimer's disease are not fully understood. This study aims at identifying conformational differences among four variants full‐length Aβ42 known display very different properties. By extensive all‐atom Monte Carlo simulations, we find a variety β‐sheet structures distinct turns readily accessible for Aβ42. In wild type (WT) preferentially populates two major classes conformations, either extended high...

We present and study a minimal structure-based model for the self-assembly of peptides into ordered β-sheet-rich fibrils. The are represented by unit-length sticks on cubic lattice interact hydrogen bonding hydrophobicity forces. Using Monte Carlo simulations with >10(5) peptides, we show that fibril formation occurs sigmoidal kinetics in model. To determine mechanism nucleation, compute joint distribution length width aggregates at equilibrium, using an efficient cluster move flat-histogram...

Quantum annealing has shown promise for finding solutions to difficult optimization problems, including protein folding. Recently, we used the D-Wave Advantage quantum annealer explore folding problem in a coarse-grained lattice model, HP which amino acids are classified into two broad groups: hydrophobic (H) and polar (P). Using set of 22 sequences with up 64 acids, demonstrated fast consistent identification correct model ground states using hybrid quantum-classical solver. An equally...

Abstract A reduced protein model with five to six atoms per amino acid and types is developed tested on a three‐helix‐bundle protein, 46‐amino fragment from staphylococcal A. The does not rely the widely used Gō approximation, which ignores non‐native interactions. We find that collapse transition considerably more abrupt for sequence than random sequences same composition. chain found be at least as fast helix formation. Energy minimization restricted thermodynamically favored topology...

Abstract Using all‐atom Monte Carlo simulations with implicit water, combined a cluster size analysis, we study the aggregation of Aβ 16 –22 , peptide capable forming amyloid fibrils. We consider system six initially randomly oriented peptides, and investigate thermodynamics structural properties aggregates formed by this system. The is unaggregated without ordered secondary structure at high temperature, forms β‐sheet rich low temperature. At crossover between these two regimes, find that...

On the surface of it: Experimental and computational analyses for a hybrid peptide–substrate system showed that changing position proline residue in synthetic peptides changes their adsorption onto semiconductors substantially predictably (see picture with Si(100) surface). Such information is essential formation novel peptide–solid interfaces nanotechnological applications. Detailed facts importance to specialist readers are published as "Supporting Information". documents peer-reviewed,...

Abstract The α‐synuclein protein (αS), implicated in Parkinson's disease, shows conformational versatility. It aggregates into β‐sheet‐rich fibrils, occurs helical membrane‐bound forms, is disordered as a free monomer, and has recently been suggested to have folded tetramer its main physiological form. Here, we use implicit solvent all‐atom Monte Carlo methods explore the ensemble sampled by αS monomer. We analyze secondary structure propensities, size, topological properties compare with...