On the Need for Phenomenological Theory of P-Vortices or Does Spaghetti Confinement Pattern Admit Condensed-Matter Analogies?

Usually the intuition from condensed-matter physics is used to provide ideas for possible confinement mechanisms in gauge theories. Today, with a clear but puzzling ``spaghetti'' confinement pattern, arising after a decade of lattice computer experiments, which implies formation of a fluctuating net of peculiar magnetic vortices rather than condensation of the homogeneously distributed magnetic monopoles, the time is coming to reverse the logic and search for similar patterns in condensed matter systems. The main thing to look for in a condensed matter setup is the simultaneous existence of narrow tubes ($P$-vortices or 1-branes) of direction-changing electric field and broader tubes (Abrikosov lines) of magnetic field, a pattern dual to the one, presumably underlying confinement in gluodynamics. As a possible place for this search we suggest systems with coexisting charge-density waves and superconductivity.Comment: 20 pages, 7 figures; to be published in ZhET

Non-Perturbative Dynamics in Supersymmetric Gauge Theories

I give an introductory review of recent, fascinating developments in supersymmetric gauge theories. I explain pedagogically the miraculous properties of supersymmetric gauge dynamics allowing one to obtain exact solutions in many instances. Various dynamical regimes emerging in supersymmetric Quantum Chromodynamics and its generalizations are discussed. I emphasize those features that have a chance of survival in QCD and those which are drastically different in supersymmetric and non-supersymmetric gauge theories. Unlike most of the recent reviews focusing almost entirely on the progress in extended supersymmetries (the Seiberg-Witten solution of N=2 models), these lectures are mainly devoted to N=1 theories. The primary task is extracting lessons for non-supersymmetric theories.Comment: 121 pages, LATEX, epsfig, 4 figures. Several typos corrected and references added. Extended version of lectures given at International School of Physics "Enrico Fermi", Varenna, Italy, July 3-6, 1995; Institute of Nuclear Science, UNAM, Mexico, April 11-17, 1996, and Summer School in High-Energy Physics and Cosmology, 10 - 26 July, 1996, ICTP, Triest, Ital

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins

Natural proteins often partake in several highly specific protein-protein interactions. They are thus subject to multiple opposing forces during evolutionary selection. To be functional, such multispecific proteins need to be stable in complex with each interaction partner, and, at the same time, to maintain affinity toward all partners. How is this multispecificity acquired through natural evolution? To answer this compelling question, we study a prototypical multispecific protein, calmodulin (CaM), which has evolved to interact with hundreds of target proteins. Starting from high-resolution structures of sixteen CaM-target complexes, we employ state-of-the-art computational methods to predict a hundred CaM sequences best suited for interaction with each individual CaM target. Then, we design CaM sequences most compatible with each possible combination of two, three, and all sixteen targets simultaneously, producing almost 70,000 low energy CaM sequences. By comparing these sequences and their energies, we gain insight into how nature has managed to find the compromise between the need for favorable interaction energies and the need for multispecificity. We observe that designing for more partners simultaneously yields CaM sequences that better match natural sequence profiles, thus emphasizing the importance of such strategies in nature. Furthermore, we show that the CaM binding interface can be nicely partitioned into positions that are critical for the affinity of all CaM-target complexes and those that are molded to provide interaction specificity. We reveal several basic categories of sequence-level tradeoffs that enable the compromise necessary for the promiscuity of this protein. We also thoroughly quantify the tradeoff between interaction energetics and multispecificity and find that facilitating seemingly competing interactions requires only a small deviation from optimal energies. We conclude that multispecific proteins have been subjected to a rigorous optimization process that has fine-tuned their sequences for interactions with a precise set of targets, thus conferring their multiple cellular functions

Light cone QCD sum rules study of the semileptonic heavy ΞQ\Xi_{Q} and ΞQ′\Xi'_{Q} transitions to Ξ\Xi and Σ\Sigma baryons

The semileptonic decays of heavy spin--1/2, $\Xi_{b(c)}$ and $\Xi'_{b(c)}$ baryons to the light spin-- 1/2, $\Xi$ and $\Sigma$ baryons are investigated in the framework of the light cone QCD sum rules. In particular, using the most general form of the interpolating currents for the heavy baryons as well as the distribution amplitudes of the $\Xi$ and $\Sigma$ baryons, we calculate all form factors entering the matrix elements of the corresponding effective Hamiltonians in full QCD. Having calculated the responsible form factors, we evaluate the decay rates and branching fractions of the related transitions.Comment: 30 Pages, 5 Figures and 18 Table

Supersymmetry and Duality in Field Theory and String Theory

This is a set of lectures given at the 99' Cargese Summer School: Particle Physics : Ideas and Recent Developments. They contain a pedestrian exposition of recent theoretical progress in non-perturbative field theory and string theory based on ideas of duality.Comment: JHEP LateX, 56 pages, 13 eps figures;v2 References adde

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Heme-heme and heme-protein interactions inside de novo-designed four-helix bundle proteins

Experimental explorations of functional mechanism of natural heme proteins are often frustrated by the fragility and complexity of these natural systems. Many of the experimental difficulties can be overcome by designing and synthesizing simplified model proteins, maquettes of complicated natural counterparts. These synthetic heme binding peptides display the significant advantages of small size, simple and easily changeable amino acid composition, high water solubility, and extraordinary stability over a wide range of conditions, while maintaining a low dielectric interior in contact with the heme. We use UV-visible, CD, Raman and FTIR spectroscopies together with redox potentiometry to investigate how the surrounding protein matrix influences the properties of heme cofactors. We explore the role of steric and electrostatic interactions in determining heme binding to synthetic peptides and achieve the Kd values in the 10–10 M range, comparable to natural heme proteins. Inside heme protein maquettes we reproduce proton coupled redox reactions with large redox-linked pK shifts from 4.2 to 7.0 and from 9.3 to 10.4 in the maquette associated side chains. This phenomena is frequently encountered but not fully understood in natural redox proteins. In maquettes, the redox-linked pK shift below pH 8 has been attributed to protonation of glutamate side chains in heme vicinity, with the closest to the heme glutamate having the major effect. The pK shift above pH 8 is thought to be due to protonation of lysine side chains. By substitution of several specific glutamates; for glutamines we eliminate redox-linked proton exchange inside maquettes, thus achieving control over H+/e- coupling. Finally, we explore different factors governing heme redox potential inside heme protein maquettes. By incorporating various natural and synthetic porphyrins into maquettes, inserting charges in heme vicinity, modifying cofactor-cofactor interactions, and varying protonation state of protein side chains, we can adjust the redox midpoint potential over 350 mV within the natural cytochrome range of 800 mV. While learning to manipulate heme binding, redox, and proton coupling properties, we are moving towards the implementation of fully functional de novo designed proteins

Heme-heme and heme-protein interactions inside de novo-designed four-helix bundle proteins

Experimental explorations of functional mechanism of natural heme proteins are often frustrated by the fragility and complexity of these natural systems. Many of the experimental difficulties can be overcome by designing and synthesizing simplified model proteins, maquettes of complicated natural counterparts. These synthetic heme binding peptides display the significant advantages of small size, simple and easily changeable amino acid composition, high water solubility, and extraordinary stability over a wide range of conditions, while maintaining a low dielectric interior in contact with the heme. We use UV-visible, CD, Raman and FTIR spectroscopies together with redox potentiometry to investigate how the surrounding protein matrix influences the properties of heme cofactors. We explore the role of steric and electrostatic interactions in determining heme binding to synthetic peptides and achieve the Kd values in the 10–10 M range, comparable to natural heme proteins. Inside heme protein maquettes we reproduce proton coupled redox reactions with large redox-linked pK shifts from 4.2 to 7.0 and from 9.3 to 10.4 in the maquette associated side chains. This phenomena is frequently encountered but not fully understood in natural redox proteins. In maquettes, the redox-linked pK shift below pH 8 has been attributed to protonation of glutamate side chains in heme vicinity, with the closest to the heme glutamate having the major effect. The pK shift above pH 8 is thought to be due to protonation of lysine side chains. By substitution of several specific glutamates; for glutamines we eliminate redox-linked proton exchange inside maquettes, thus achieving control over H+/e- coupling. Finally, we explore different factors governing heme redox potential inside heme protein maquettes. By incorporating various natural and synthetic porphyrins into maquettes, inserting charges in heme vicinity, modifying cofactor-cofactor interactions, and varying protonation state of protein side chains, we can adjust the redox midpoint potential over 350 mV within the natural cytochrome range of 800 mV. While learning to manipulate heme binding, redox, and proton coupling properties, we are moving towards the implementation of fully functional de novo designed proteins