Ground State Spin Logic

Designing and optimizing cost functions and energy landscapes is a problem encountered in many fields of science and engineering. These landscapes and cost functions can be embedded and annealed in experimentally controllable spin Hamiltonians. Using an approach based on group theory and symmetries, we examine the embedding of Boolean logic gates into the ground state subspace of such spin systems. We describe parameterized families of diagonal Hamiltonians and symmetry operations which preserve the ground state subspace encoding the truth tables of Boolean formulas. The ground state embeddings of adder circuits are used to illustrate how gates are combined and simplified using symmetry. Our work is relevant for experimental demonstrations of ground state embeddings found in both classical optimization as well as adiabatic quantum optimization.Comment: 6 pages + 3 pages appendix, 7 figures, 1 tabl

Analysis of the Equilibrium and Kinetics of the Ankyrin Repeat Protein Myotrophin

We apply the Wako-Saito-Munoz-Eaton model to the study of Myotrophin, a small ankyrin repeat protein, whose folding equilibrium and kinetics have been recently characterized experimentally. The model, which is a native-centric with binary variables, provides a finer microscopic detail than the Ising model, that has been recently applied to some different repeat proteins, while being still amenable for an exact solution. In partial agreement with the experiments, our results reveal a weakly three-state equilibrium and a two-state-like kinetics of the wild type protein despite the presence of a non-trivial free-energy profile. These features appear to be related to a careful "design" of the free-energy landscape, so that mutations can alter this picture, stabilizing some intermediates and changing the position of the rate-limiting step. Also the experimental findings of two alternative pathways, an N-terminal and a C-terminal one, are qualitatively confirmed, even if the variations in the rates upon the experimental mutations cannot be quantitatively reproduced. Interestingly, folding and unfolding pathway appear to be different, even if closely related: a property that is not generally considered in the phenomenological interpretation of the experimental data.Comment: 27 pages, 7 figure

Computational Modeling for the Ag Nanoparticle Coalescence Process: A Case of Surface Plasmon Resonance

Motivated by recent transmission electron microscopy (TEM) experiments on α-Ag2WO4, the coalescence process of Ag nanoparticles (NPs) is investigated using molecular dynamics (MD) simulations. These Ag NPs are formed by irradiation of α-Ag2WO4 crystals by electrons from a TEM gun. This behavior can be considered as a clear example of surface plasmon resonance (SPR), in which Ag NP coalescence processes are controlled by dipole–dipole interaction forming larger clusters. The interactions between Ag NPs along the coalescence processes are studied using MD simulations with embedded atom method (EAM) effective potentials for Ag. With these choices of methods, coalescence is studied by addressing different scenarios for the interacting NPs, which all could possibly occur in experiments

Mapping the topography of a protein energy landscape

Protein energy landscapes are highly complex, yet the vast majority of states within them tend to be invisible to experimentalists. Here, using site-directed mutagenesis and exploiting the simplicity of tandem-repeat protein structures, we delineate a network of these states and the routes between them. We show that our target, gankyrin, a 226-residue 7-ankyrin-repeat protein, can access two alternative (un)folding pathways. We resolve intermediates as well as transition states, constituting a comprehensive series of snapshots that map early and late stages of the two pathways and show both to be polarized such that the repeat array progressively unravels from one end of the molecule or the other. Strikingly, we find that the protein folds via one pathway but unfolds via a different one. The origins of this behavior can be rationalized using the numerical results of a simple statistical mechanics model that allows us to visualize the equilibrium behavior as well as single-molecule folding/unfolding trajectories, thereby filling in the gaps that are not accessible to direct experimental observation. Our study highlights the complexity of repeat-protein folding arising from their symmetrical structures; at the same time, however, this structural simplicity enables us to dissect the complexity and thereby map the precise topography of the energy landscape in full breadth and remarkable detail. That we can recapitulate the key features of the folding mechanism by computational analysis of the native structure alone will help toward the ultimate goal of designed amino-acid sequences with made-to-measure folding mechanisms—the Holy Grail of protein folding

Exploring the “Middle Earth” of network spectra via a Gaussian matrix function

We study a Gaussian matrix function of the adjacency matrix of artificial and real-world networks. We motivate the use of this function on the basis of a dynamical process modeled by the time-dependent Schrodinger equation with a squared Hamiltonian. In particular, we study the Gaussian Estrada index - an index characterizing the importance of eigenvalues close to zero. This index accounts for the information contained in the eigenvalues close to zero in the spectra of networks. Such method is a generalization of the so-called "Folded Spectrum Method" used in quantum molecular sciences. Here we obtain bounds for this index in simple graphs, proving that it reaches its maximum for star graphs followed by complete bipartite graphs. We also obtain formulas for the Estrada Gaussian index of Erdos-Renyi random graphs as well as for the Barabasi-Albert graphs. We also show that in real-world networks this index is related to the existence of important structural patters, such as complete bipartite subgraphs (bicliques). Such bicliques appear naturally in many real-world networks as a consequence of the evolutionary processes giving rise to them. In general, the Gaussian matrix function of the adjacency matrix of networks characterizes important structural information not described in previously used matrix functions of graphs

USE OF A HOMEOPATHIC PRODUCT IN DOGS REDUCES THE NEGATIVE EFFECTS OF CANINE ATOPIC DERMATITIS

This study aimed to determine whether a homeopathic product formulated based on Hepar sulfur, Rhus toxicodendron, Graphites, and Urtica urens would prevent atopic dermatitis in dogs. Ten male beagle dogs were used, divided into two groups with five repetitions per group. The control (CO) animals received a diet with 0.5 mL/day of placebo for 30 consecutive days in a preventive manner, and we later added ethoxyquin at 0.4 mg/day. The treated group (TRA) received a ration with 0.5 mL/day of homeopathic for 30 consecutive days as a preventive, and we later added ethoxyquin at 0.4 mg/day. Blood samples were collected on days 1, 30, and 40 to analyze antioxidant and oxidant status. In an ethogram, the presence of a crusted lesion, alopecic lesion, or hair loss were evaluated at three timepoints: pre-challenge, 5, and 10 days post-challenge. No lesions were observed in the pre-challenge period. Dogs fed the homeopathic on day 5 after challenge presented 40% less crusted lesion and 60% less hair loss than the control. Nitric oxide (NOx) and reactive oxygen species (ROS) levels increased over time in both groups (P < 0.001). On day 40 of the experiment, lower levels of NOx (P < 0.001) and ROS (P < 0.025) were observed in the TRA group than in the CO group. In contrast, glutathione S-transferase activity increased over time in both groups (P < 0.001); however, this increase on day 40 was more significant in the dogs in the treated group than in the control (P < 0.010). We conclude that the preventive addition of homeopathic reduced the incidence of skin lesions and prevented oxidative stress caused by canine atopic dermatitis

Fast and real-time electrical transistor assay for quantifying SARS-CoV-2 neutralizing antibodies

Due to the SARS-CoV-2 pandemic renewed attention has been directed towards viral neutralization assays and neutralizing antibodies quantification, for vaccine pre-clinical trials and determining vaccine efficacy over time. The gold standard to assess antibody titer is the plaque reduction neutralization test, an end-point assay which evaluates the highest serum antibody dilution that neutralizes viral replication, by inspecting the cytopathic effect induced on cell cultures. Here, we use planar, PEDOT:PSS-based organic electrochemical transistors for real-time, remote-controlled, reliable and fast electrical monitoring of the cytopathic effect induced by SARS29 CoV-2 on Vero E6 cell lines, allowing the quantification of serum neutralizing titer. Our low-cost and scalable device has the potential to speed-up large-scale viral neutralization screening without the need for cancerous staining or highly specialized operators. Finally, the technology could be easily transferred to assess neutralizing antibody response towards different viruses in their permissive cell substrates

Effects of different diet alternatives to replace the use of pharmacological levels of zinc on growth performance and fecal dry matter of weanling pigs

A total of 300 weanling pigs (Line 400 × 200, DNA, Columbus, NE, initially 4.83 kg) were used in a 46-d trial to evaluate the effects of different nutritional strategies to replace pharmacological levels of Zn, provided by zinc oxide (ZnO), in nursery diets on growth performance and fecal dry matter (DM). Six treatments with 10 replicate pens per treatment and 5 pigs per pen were used. Diets consisted of: (1) positive control (ZnO providing 3,000 mg/kg added Zn from d 0 to 7 and 2,000 mg/kg added Zn from d 8 to 25 and 21% crude protein, CP); (2) negative control (NC; no added ZnO); (3) NC plus 1.2% Na diformate; (4) NC with 4% coarse ground wheat bran; (5) NC but formulated to 18% CP; and (6) the combination of NC with 18% CP, 1.2% Na diformate, and 4% coarse ground wheat bran. The diets formulated to 18% CP contained 1.2% standardized ileal digestible (SID) Lys from d 0 to 25, whereas the 21% CP diets contained 1.4% SID Lys from d 0 to 7 and 1.35% SID Lys from d 7 to 25. From d 25 to 46, all pigs were fed a common diet. From d 0 to 7, no differences in any variables were observed between treatments. From d 7 to 25, pigs fed the diet with added ZnO had greater (P < 0.01) average daily gain (ADG) and average daily feed intake (ADFI) than all other treatments. Pigs fed the diet formulated to 18% CP had decreased (P < 0.01) ADG when compared with pigs fed the other diets. From d 25 to 46, no previous treatment effects on ADG or gain to feed ratio (G:F) were observed. Overall (d 0 to 46), pigs fed the diet with added ZnO from d 0 to 25 had greater (P < 0.01) ADG, ADFI, and final body weight than pigs fed added Na Diformate, or 4% coarse ground wheat bran, or with the 18% CP diet, or with pigs fed the combination of the additives intermediate. There was no evidence for differences in overall G:F. Pigs fed the NC diet had the lowest fecal DM and highest fecal scores (P < 0.05), indicating the greatest incidence of loose stools. Pigs fed added ZnO had greater fecal DM than pigs fed the NC, 4% added wheat bran, or 18% CP diets, or with pigs fed the combination of additives intermediate (P < 0.01). These results suggest that adding pharmacological levels of Zn from ZnO improves nursery pig performance and increases DM content of feces when compared with pigs fed diets with either Na diformate, 4% course wheat bran, or 18% CP alone. However, a combination of all three alternatives appeared to be additive and partially restored growth performance similar to adding pharmacological levels of Zn