1,179 research outputs found
Freezing in random graph ferromagnets
Using T=0 Monte Carlo and simulated annealing simulation, we study the energy
relaxation of ferromagnetic Ising and Potts models on random graphs. In
addition to the expected exponential decay to a zero energy ground state, a
range of connectivities for which there is power law relaxation and freezing to
a metastable state is found. For some connectivities this freezing persists
even using simulated annealing to find the ground state. The freezing is caused
by dynamic frustration in the graphs, and is a feature of the local
search-nature of the Monte Carlo dynamics used. The implications of the
freezing on agent-based complex systems models are briefly considered.Comment: Published version: 1 reference deleted, 1 word added. 4 pages, 5
figure
Dynamical frustration in ANNNI model and annealing
Zero temperature quench in the Axial Next Nearest Neighbour Ising (ANNNI)
model fails to bring it to its ground state for a certain range of values of
the frustration parameter , the ratio of the next nearest neighbour
antiferromagnetic interaction strength to the nearest neighbour one. We apply
several annealing methods, both classical and quantum, and observe that the
behaviour of the residual energy and the order parameter depends on the value
of strongly. Classical or thermal annealing is found to be adequate
for small values of .
However, neither classical nor quantum annealing is effective at values of
close to the fully frustrated point , where the residual
energy shows a very slow algebraic decay with the number of MCS.Comment: 6 pages,10 figures, to be published in Proceedings of " The
International Workshop on Quantum annealing and other Optimization Methods
Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin
BACKGROUND: Many biologically active compounds bind to plasma transport proteins, and this binding can be either advantageous or disadvantageous from a drug design perspective. Human serum albumin (HSA) is one of the most important transport proteins in the cardiovascular system due to its great binding capacity and high physiological concentration. HSA has a preference for accommodating neutral lipophilic and acidic drug-like ligands, but is also surprisingly able to bind positively charged peptides. Understanding of how short cationic antimicrobial peptides interact with human serum albumin is of importance for developing such compounds into the clinics. RESULTS: The binding of a selection of short synthetic cationic antimicrobial peptides (CAPs) to human albumin with binding affinities in the μM range is described. Competitive isothermal titration calorimetry (ITC) and NMR WaterLOGSY experiments mapped the binding site of the CAPs to the well-known drug site II within subdomain IIIA of HSA. Thermodynamic and structural analysis revealed that the binding is exclusively driven by interactions with the hydrophobic moieties of the peptides, and is independent of the cationic residues that are vital for antimicrobial activity. Both of the hydrophobic moieties comprising the peptides were detected to interact with drug site II by NMR saturation transfer difference (STD) group epitope mapping (GEM) and INPHARMA experiments. Molecular models of the complexes between the peptides and albumin were constructed using docking experiments, and support the binding hypothesis and confirm the overall binding affinities of the CAPs. CONCLUSIONS: The biophysical and structural characterizations of albumin-peptide complexes reported here provide detailed insight into how albumin can bind short cationic peptides. The hydrophobic elements of the peptides studied here are responsible for the main interaction with HSA. We suggest that albumin binding should be taken into careful consideration in antimicrobial peptide studies, as the systemic distribution can be significantly affected by HSA interactions
The random K-satisfiability problem: from an analytic solution to an efficient algorithm
We study the problem of satisfiability of randomly chosen clauses, each with
K Boolean variables. Using the cavity method at zero temperature, we find the
phase diagram for the K=3 case. We show the existence of an intermediate phase
in the satisfiable region, where the proliferation of metastable states is at
the origin of the slowdown of search algorithms. The fundamental order
parameter introduced in the cavity method, which consists of surveys of local
magnetic fields in the various possible states of the system, can be computed
for one given sample. These surveys can be used to invent new types of
algorithms for solving hard combinatorial optimizations problems. One such
algorithm is shown here for the 3-sat problem, with very good performances.Comment: 38 pages, 13 figures; corrected typo
A GA microsatellite in the Fli1 promoter modulates gene expression and is associated with systemic lupus erythematosus patients without nephritis
Ising model in small-world networks
The Ising model in small-world networks generated from two- and
three-dimensional regular lattices has been studied. Monte Carlo simulations
were carried out to characterize the ferromagnetic transition appearing in
these systems. In the thermodynamic limit, the phase transition has a
mean-field character for any finite value of the rewiring probability p, which
measures the disorder strength of a given network. For small values of p, both
the transition temperature and critical energy change with p as a power law. In
the limit p -> 0, the heat capacity at the transition temperature diverges
logarithmically in two-dimensional (2D) networks and as a power law in 3D.Comment: 6 pages, 7 figure
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